[November 15, 2017] Understanding the evolution of the vertebrate genome using whole-genome multiple alignments

Joel Armstrong, PhD Student, Biomolecular Engineering & Bioinformatics
Wednesday, November 15, 2017 – 12:00pm
Location – Engineering 2, Room 506
Host – Professor Benedict Paten

Abstract: Large sequencing projects, such as the 200 Mammals and Bird 10K projects, will be sequencing, assembling, and analyzing hundreds of vertebrate genomes over the next year. These massive sequencing projects offer insight into vertebrate genome evolution, but many analyses will require a large, very accurate genome multiple alignment. I present a progressive extension to the Cactus genome aligner which was necessary to be able to scale to hundreds of vertebrate-sized genomes while maintaining alignment quality. In addition, I present plans to collaborate closely with the 200 Mammals project to produce the largest ever alignment of mammalian genomes, enabling extremely-high-resolution constrained element annotations on all included mammalian genomes. Finally, I present plans to use these new data to build an extremely large vertebrate-wide alignment, which I will use to analyze significant changes in mutation processes (via the analysis of “mutation signatures”) over the evolution of the vertebrate genome.